Decreasing motion artifacts in calcium-dependent fluorescence transients from the perfused mouse heart using frequency filtering

A strategy has been developed for the removal of motion artifact and noise in calcium-dependent fluorescence transients from the perfused mouse heart using frequency filtering. An analytical model indicates that the spectral removal of motion artifacts is independent of the phase shift of the motion waveform in the frequency domain, and thus to the time shift (or delay) of motion in the time domain. This is based on the "shift theorem" of Fourier analysis, which avoids erroneous correction of motion artifact when using the motion signal obtained using reflectance from the heart. Several major steps are adopted to implement this model for elimination of motion as well as detection noise from the fluorescence transient signals from the calcium-sensitive probe Rhod-2. These include (1) extracting the fluorescence calcium transient signal from the raw data by using power spectrum density (PSD) in the frequency domain by subtracting the motion recorded using the reflectance of excitation light, (2) digitally filtering out the random noise using multiple bandpass filters centralized at harmonic frequencies of the transients, and (3) extracting high frequency noise with a Gaussian Kernel filter method. The processed signal of transients acquired with excessive motion artifact is comparable to transients acquired with minimal motion obtained by immobilizing the heart against the detection window, demonstrating the usefulness of this technique.     

Bayesian denoising framework of phonocardiogram based on a new dynamical model

In this paper, we introduce a model-based Bayesian denoising framework for phonocardiogram (PCG) signals. The denoising framework is founded on a new dynamical model for PCG, which is capable of generating realistic synthetic PCG signals. The introduced dynamical model is based on PCG morphology and is inspired by electrocardiogram (ECG) dynamical model proposed by McSharry et al. and can represent various morphologies of normal PCG signals. The extended Kalman smoother (EKS) is the Bayesian filter that is used in this study. In order to facilitate the adaptation of the denoising framework to each input PCG signal, the parameters are selected automatically from the input signal itself. This approach is evaluated on several PCGs recorded on healthy subjects, while artificial white Gaussian noise is added to each signal, and the SNR and morphology of the outputs of the proposed denoising approach are compared with the outputs of the wavelet denoising (WD) method. The results of the EKS demonstrate better performance than WD over a wide range of PCG SNRs. The new PCG dynamical model can also be employed to develop other model-based processing frameworks such as heart sound segmentation and compression.     

Local estimate of surface Laplacian derivation on a realistically shaped scalp surface and its performance on noisy data

A new implementation of the surface Laplacian derivation (SLD) method is desribed which reconstructs a realistically shaped, local scalp surface geometry using measured electrode positions, generates a local spectral-interpolated potential distribution function, and estimates the surface Laplacian values through a local planar parametric space using a stable numerical method combining Taylor expansions with the least-squares technique. The implementation is modified for efficient repeated SLD operations on a time series. Examples are shown of applications to evoked potential data. The resolving power of the SLD is examined as a function of the spatial signal-to-noise (SNR) ratio. The analysis suggests that the Laplacian is effective when the spatial SNR is greater than 3. It is shown that spatial low-pass filtering with a Gaussian filter can be used to reduce the effect of noise and recover useful signal if the noise is spatially incoherent.     

Relationship Between Time- and Frequency-Domain Analyses of Angular Head Movements in the Squirrel Monkey

We used the three-dimensional magnetic search-coil recording technique to study the range of active angular head movements made by squirrel monkeys. There were two goals in this study: (1) to determine the range of angular velocities and accelerations as well as the bandwidth and other frequency characteristics of active head movements and (2) to compare analyses of transients of velocity and acceleration that are studied by residual analysis, Fourier transform, and wavelet transform of the head velocity signal.The residual analysis showed that the shape and duration of the transients affected the bandwidth. During the time after the head had begun to accelerate, the frequency content of the head movement extended into the range of 6 to 12 Hz. When considering all three planes of rotation, approximately 75% of the transients had peak acceleration between 2,000 and 10,000 deg/s² and a peak velocity of 50 to 400 deg/s. A peak acceleration of >10,000 deg/s² was recorded in 10% of the transients.These findings indicate that active head movements in squirrel monkeys cover a higher range of frequencies, accelerations, and velocities than have typically been used in previous eye-movement and neuronal studies of the reflexes that control gaze. We further conclude that the choice of a method for analyzing transient, time-varying biological signals is dependent on the desired information. Residual analysis provides detailed resolution in the time domain, but estimation of the frequency content of the signal is dependent on the portions selected for analysis and the choice of filters. Fourier transform provides a representation of the power spectrum in the frequency domain but without any inherent temporal resolution. We show that the wavelet transform, a novel method as applied to the signal analysis goals of this study, is the most useful technique for relating time- and frequency-domain information during a continuous signal.     

Vbmp: variational Bayesian Multinomial Probit Regression for multi-class classification in R

SUMMARY: Vbmp is an R package for Gaussian Process classification of data over multiple classes. It features multinomial probit regression with Gaussian Process priors and estimates class posterior probabilities employing fast variational approximations to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. Being equipped with only one main function and reasonable default values for optional parameters, vbmp combines flexibility with ease of usage as is demonstrated on a breast cancer microarray study. AVAILABILITY: The R library vbmp implementing this method is part of Bioconductor and can be downloaded from http://www.dcs.gla.ac.uk/~girolami     

Responses of Ca2+-binding proteins to localized,transient changes in intracellular [Ca2+

In smooth muscle cells, various transient, localized [Ca(2+)] changes have been observed that are thought to regulate cell function without necessarily inducing contraction. Although a great deal of effort has been put into detecting these transients and elucidating the mechanisms involved in their generation, the extent to which these transient Ca(2+) signals interact with intracellular Ca(2+)-binding molecules remains relatively unknown. To understand how the spatial and temporal characteristics of an intracellular Ca(2+) signal influence its interaction with Ca(2+)-binding proteins, mathematical models of Ca(2+) diffusion and regulation in smooth muscle cells were used to study Ca(2+) binding to prototypical proteins with one or two Ca(2+)-binding sites. Simulations with the models: (1) demonstrate the extent to which the rate constants for Ca(2+)-binding to proteins and the spatial and temporal characteristics of different Ca(2+) transients influence the magnitude and time course of the responses of these proteins to the transients; (2) predict significant differences in the responses of proteins with one or two Ca(2+)-binding sites to individual Ca(2+) transients and to trains of transients; (3) demonstrate how the kinetic characteristics determine the fidelity with which the responses of Ca(2+)-sensitive molecules reflect the magnitude and time course of transient Ca(2+) signals. Overall, this work demonstrates the clear need for complete information about the kinetics of Ca(2+) binding for determining how well Ca(2+)-binding molecules respond to different types of Ca(2+) signals. These results have important implications when considering the possible modulation of Ca(2+)- and Ca(2+)/calmodulin-dependent proteins by localized intracellular Ca(2+) transients in smooth muscle cells and, more generally, in other cell types.     

Nonstationary Heart Rate Variability in Respiratory Tests

A new method was proposed for processing a nonstationary heart rate by using frequency-modulated signals rather than amplitude-modulated signals equally spaced over several points of time as in the conventional method. A frequency-modulated signal is a set of identical Gaussian peaks that coincide with the true time points of heart beats. A continuous wavelet transform was used to quantitatively describe the heart rhythm signal. A test with controlled breathing was performed as an example and included three consecutive stages: rest, rhythmic breathing at a specified frequency, and exhalation. Tachograms recorded during the breath test was found to be a nonstationary signal with the alternation of peaks of different spectral ranges. A system of quantitative parameters was developed to describe the dynamics of changes in the spectral properties of the tachogram in transitional areas. A static clustering by the effect of the respiratory test and a dynamic clustering in order to identify the time points when the autonomic nervous system is stressed were performed for all subjects. The article discusses the prospects of using the method as a means to analyze the transient effects in various functional tests and as biofeedback that would help to change the heart rhythm.     

Using Gaussian process with test rejection to detect T-cell epitopes in pathogen genomes

A major challenge in the development of peptide-based vaccines is finding the right immunogenic element, with efficient and long-lasting immunization effects, from large potential targets encoded by pathogen genomes. Computer models are convenient tools for scanning pathogen genomes to preselect candidate immunogenic peptides for experimental validation. Current methods predict many false positives resulting from a low prevalence of true positives. We develop a test reject method based on the prediction uncertainty estimates determined by Gaussian process regression. This method filters false positives among predicted epitopes from a pathogen genome. The performance of stand-alone Gaussian process regression is compared to other state-of-the-art methods using cross validation on 11 benchmark data sets. The results show that the Gaussian process method has the same accuracy as the top performing algorithms. The combination of Gaussian process regression with the proposed test reject method is used to detect true epitopes from the Vaccinia virus genome. The test rejection increases the prediction accuracy by reducing the number of false positives without sacrificing the method's sensitivity. We show that the Gaussian process in combination with test rejection is an effective method for prediction of T-cell epitopes in large and diverse pathogen genomes, where false positives are of concern.     

Analysis of ECG signal denoising method based on S-transform

Electrocardiogram (ECG), a noninvasive technique which is used generally as a primary diagnostic tool for cardiovascular diseases. A cleaned ECG signal provides necessary information about the electrophysiology of the heart diseases and ischemic changes that may occur. However in real situation, noise is often embedded with ECG signal during acquisition. In this paper, a novel ECG signal denoising technique is proposed using Stockwell transform (S-transform). This method is evaluated on several normal and abnormal ECG signals of MIT/BIH arrhythmia database, by artificially adding white Gaussian noises to visually inspected clean ECG recordings. The experimental results demonstrate that the proposed method shows the better signal to noise ratio (SNR), lower root mean square error (RMSE) and percent root mean square difference (PRD) compared to generally used ECG denoising method like wavelet transform.     

A novel theoretical approach to the analysis of dendritic transients.

A novel theoretical framework for analyzing dendritic transients is introduced. This approach, called the method of moments, is an extension of Rall's cable theory for dendrites. It provides analytic investigation of voltage attenuation, signal delay, and synchronization problems in passive dendritic trees. In this method, the various moments of a transient signal are used to characterize the properties of the transient. The strength of the signal is measured by the time integral of the signal, its characteristic time is determined by its centroid ("center of gravity"), and the width of the signal is determined by a measure similar to the standard deviation in probability theory. Using these signal properties, the method of moments provides theorems, expressions, and efficient algorithms for analyzing the voltage response in arbitrary passive trees. The method yields new insights into spatiotemporal integration, coincidence detection mechanisms, and the properties of local interactions between synaptic inputs in dendritic trees. The method can also be used for matching dendritic neuron models to experimental data and for the analysis of synaptic inputs recorded experimentally.     

Simultaneous recording of calcium transients in skeletal muscle using high- and low-affinity calcium indicators.

To monitor cytosolic [Ca2+] over a wide range of concentrations in functioning skeletal muscle cells, we have used simultaneously the rapid but relatively low affinity calcium indicator antipyrylazo III (AP III) and the slower but higher affinity indicator fura-2 in single frog twitch fibers cut at both ends and voltage clamped with a double vaseline gap system. When both dyes were added to the end pool solution the cytosolic fura-2 concentration reached a steady level equal to the end pool concentration within approximately 2.5 h, a time when the AP III concentration was still increasing. For depolarizing pulses of increasing amplitude, the fura-2 fluorescence signal approached saturation when the simultaneously recorded AP III absorbance change was far from saturation. Comparison of simultaneously recorded fura-2 and AP III signals indicated that the mean values of the on and off rate constants for calcium binding to fura-2 in 18 muscle fibers were 1.49 x 10(8) M-1 s-1 and 11.9 s-1, respectively (mean KD = 89 nM), if all AP III in the fiber is assumed to behave as in calibrating solution and to be in instantaneous equilibrium with [Ca2+]. [Ca2+] transients calculated from the fura-2 signals using these rate constants were consistent with the [Ca2+] transients calculated from the AP III signals. Resting [Ca2+] or small changes in [Ca2+] which could not be reliably monitored with AP III could be monitored with fura-2 with little or no interference from changes in [Mg2+] or from intrinsic signals. The fura-2 signal was also less sensitive to movement artifacts than the AP III signal. After a [Ca2+] transient the fura-2 signal demonstrated a relatively small elevation of [Ca2+] that was maintained for many seconds.     

Fetal ECG extraction during labor using an adaptive maternal beat subtraction technique.

Fetal ECG (FECG) monitoring using abdominal maternal signals is a non-invasive technique that allows early detection of changes in fetal wellbeing. Several other signal components have stronger energy than the FECG, the most important being maternal ECG (MECG) and, especially during labor, uterine EMG. This study proposes a new method to subtract MECG after detecting and removing abdominal signal segments with high-amplitude variations due to uterine contractions. The method removes MECG from abdominal signals using an approximation of the current MECG segment based on a linear combination of previous MECG segments aligned on the R-peak. The coefficients of the linear model are computed so that the squared error of the approximation over the whole current segment is minimized. Abdominal signal segments strongly affected by uterine contractions are detected by applying median filtering. The methods proposed are tested on real abdominal data recorded during labor, with FECG recorded using scalp electrodes synchronously recorded for comparison.     

Abundance Estimation With a Transient Model Under the Robust Design

Abstract: A common situation in capture-mark-recapture (CMR) studies on birds and other organisms is to capture individuals not belonging to the studied population only present during the short time of the capture session. Presence of such transient individuals affects demographic parameter estimation from CMR data. Methods exist to reduce biases on survival estimates in the presence of transients and have been shown to be particularly efficient within the Robust Design framework (several secondary capture sessions within a short time interval during which the studied population can be assumed closed). We present a new model to estimate population size accounting for transients. We first used simulated data to show that the method reduces positive biases due to transients. In a second step, we applied the method to a real CMR dataset on a reed warbler (Acrocephalus scirpaceus) population. Population size estimates are reduced by up to 50% when correcting for the presence of transients. Many field studies on managed animal populations use capture-recapture methodology to obtain crucial parameters of the focal population demography. The resulting data sets are used either to estimate population size ignoring the presence of transients, or to estimate vital rates, accounting for transients but overlooking abundance estimation. Our method conciliates these 2 approaches.     

Nonproton ion release by purple membranes exhibits cooperativity as shown by determination of the optical cross-section.

The amplitudes of the conductivity transients in photoexcited purple membranes were studied as a function of the energy of the actinic flash to determine the optical cross section of the process giving rise to the conductivity transient. Heating of the solution by the absorbed light causes an additional conductivity change and serves as an internal actinometer; the experiment directly yields the ratio of the cross section of ion release/uptake to that for light absorption. In effect, this counts the number of bacteriorhodopsin (bR) molecules involved in the conductivity transient per photon absorbed. At pH 7 in 0.4-0.5 M NaCl, where the conductivity signals are dominated by nonproton ions, the ratio is between 3 and 4, i.e., excitation of any one of several chromophores generates the same ion release signal. The simplest interpretation is that at pH 7 cooperative conformational changes cause a transient change in the surface charge distribution near all the affected bR molecules, resulting in the transient release of numerous counterions. As a comparison, at pH 4 where the signals are due to protons alone, the cross section data indicate that only a single bR molecule is involved in the proton movements. In this case, the results also show that the sum of the primary forward and reverse quantum yields (for the reactions: bR----K) is 0.88 +/- 0.09.     

Location of innervation zone determined with multichannel surface electromyography using an optical flow technique.

Multichannel surface electromyography has developed towards more channels and higher spatial resolution. This allows the study of multichannel electromyograms as images of the potential distribution on the skin. In this paper, a method that estimates the motion of the potential distribution using an optical-flow-based technique is introduced. The optical flow is a vector field that describes how images change with time. The aim of this study was to introduce a new method for innervation zone (IZ) localization and to evaluate its performance. The new method was compared with a method that uses the position of the lowest root-mean-square (RMS) value in an electrode array as an estimate of the IZ localization. Comparisons were made with both simulated signals and with recorded multichannel electromyogram signals. Simulations showed that the methods performed similarly for high signal-to-noise ratio (SNR) and that the optical-flow-based method was superior for lower SNR. When the experimental signals were used, localization with the optical-flow-based method gave a mean absolute deviation of 2.4mm from the location given by an expert group. The lowest RMS method gave a significantly higher deviation (13.6mm). Due to the low computational complexity of the optical flow algorithm it is possible to get the estimations of the IZ localization in real time.     

Mitochondria fine-tune the slow Ca(2+) transients induced by electrical stimulation of skeletal myotubes

Mitochondria sense cytoplasmic Ca(2+) signals in many cell types. In mammalian skeletal myotubes, depolarizing stimuli induce two independent cytoplasmic Ca(2+) signals: a fast signal associated with contraction and a slow signal that propagates to the nucleus and regulates gene expression. How mitochondria sense and possibly affect these cytoplasmic Ca(2+) signals has not been reported. We investigated here (a) the emergence of mitochondrial Ca(2+) signals in response to electrical stimulation of myotubes, (b) the contribution of mitochondrial Ca(2+) transients to ATP generation and (c) the influence of mitochondria as modulators of cytoplasmic and nuclear Ca(2+) signals. Rhod2 and Fluo3 fluorescence determinations revealed composite Ca(2+) signals associated to the mitochondrial compartment in electrically stimulated (400 pulses, 45 Hz) skeletal myotubes. Similar Ca(2+) signals were detected when using a mitochondria-targeted pericam. The fast mitochondrial Ca(2+) rise induced by stimulation was inhibited by pre-incubation with ryanodine, whereas the phospholipase C inhibitor U73122 blocked the slow mitochondrial Ca(2+) signal, showing that mitochondria sense the two cytoplasmic Ca(2+) signal components. The fast but not the slow Ca(2+) transient enhanced mitochondrial ATP production. Inhibition of the mitochondrial Ca(2+) uniporter prevented the emergence of mitochondrial Ca(2+) transients and significantly increased the magnitude of slow cytoplasmic Ca(2+) signals after stimulation. Precluding mitochondrial Ca(2+) extrusion with the Na(+)/Ca(2+) exchanger inhibitor CGP37157 decreased mitochondrial potential, increased the magnitude of the slow cytoplasmic Ca(2+) signal and decreased the rate of Ca(2+) signal propagation from one nucleus to the next. Over expression of the mitochondrial fission protein Drp-1 decreased mitochondrial size and the slow Ca(2+) transient in mitochondria, but enhanced cytoplasmic and nuclear slow transients. The present results indicate that mitochondria play a central role in the regulation of Ca(2+) signals involved in gene expression in myotubes.     

A chemical method for intracellular loading of the calcium indicator aequorin in mammalian skeletal muscle.

The bioluminescent calcium indicator aequorin was loaded into bundles of skeletal muscle fibers from the rat extensor digitorum longus by macroinjection, a technique previously applied only to cardiac muscle. After loading, the amplitude and time course of the twitch returned to control values, indicating lack of damage to the fibers. Individual light signals (i.e., calcium transients) were recorded during each twitch or tetanus without the need for signal averaging. The calcium transients obtained were qualitatively and quantitatively similar to those reported previously with microinjection of aequorin. Our data suggest that macroinjection may be the method of choice for loading aequorin into mammalian skeletal muscle.     

Automated region of interest analysis of dynamic Ca²⁺ signals in image sequences

Ca(2+) signals are commonly measured using fluorescent Ca(2+) indicators and microscopy techniques, but manual analysis of Ca(2+) measurements is time consuming and subject to bias. Automated region of interest (ROI) detection algorithms have been employed for identification of Ca(2+) signals in one-dimensional line scan images, but currently there is no process to integrate acquisition and analysis of ROIs within two-dimensional time lapse image sequences. Therefore we devised a novel algorithm for rapid ROI identification and measurement based on the analysis of best-fit ellipses assigned to signals within noise-filtered image sequences. This algorithm was implemented as a plugin for ImageJ software (National Institutes of Health, Bethesda, MD). We evaluated the ability of our algorithm to detect synthetic Gaussian signal pulses embedded in background noise. The algorithm placed ROIs very near to the center of a range of signal pulses, resulting in mean signal amplitude measurements of 99.06 ± 4.11% of true amplitude values. As a practical application, we evaluated both agonist-induced Ca(2+) responses in cultured endothelial cell monolayers, and subtle basal endothelial Ca(2+) dynamics in opened artery preparations. Our algorithm enabled comprehensive measurement of individual and localized cellular responses within cultured cell monolayers. It also accurately identified characteristic Ca(2+) transients, or Ca(2+) pulsars, within the endothelium of intact mouse mesenteric arteries and revealed the distribution of this basal Ca(2+) signal modality to be non-Gaussian with respect to amplitude, duration, and spatial spread. We propose that large-scale statistical evaluations made possible by our algorithm will lead to a more efficient and complete characterization of physiologic Ca(2+)-dependent signaling.     

A methodology for estimating the shape of biconcave red blood cells using multicolor scattering images

In this paper, a novel methodology for estimating the shape of human biconcave red blood cells (RBCs), using color scattering images, is presented. The information retrieval process includes, image normalization, features extraction using two-dimensional discrete transforms, such as angular radial transform (ART), Zernike moments and Gabor filters bank and features dimension reduction using both independent component analysis (ICA) and principal component analysis (PCA). A radial basis neural network (RBF-NN) estimates the RBC geometrical properties. The proposed method is evaluated in both regression and identification tasks by processing images of a simulated device used to acquire scattering phenomena of moving RBCs. The simulated device consists of a tricolor light source (light emitting diode – LED) and moving RBCs in a thin glass. The evaluation database includes 23,625 scattering images, obtained by means of the boundary element method. The regression and identification accuracy of the actual RBC shape is estimated using three feature sets in the presence of additive white Gaussian noise from 60 to 10 dB SNR and systematic distortion, giving a mean error rate less than 1% of the actual RBC shape, and more than 99% mean identification rate.     

Perialveolar interstitial resistance and compliance in isolated rat lung

We have developed a method to characterize fluid transport through the perialveolar interstitium using micropuncture techniques. In 10 experiments we established isolated perfused rat lung preparations. The lungs were initially isogravimetric at 10 cmH2O arterial pressure, 2 cmH2O venous pressure, and 5 cmH2O alveolar pressure. Perialveolar interstitial pressure was determined by micropuncture at alveolar junctions by use of the servo-null technique. Simultaneously a second micropipette was placed in an alveolar junction 20-40 microns away, and a bolus of albumin solution (3.5 g/100 ml) was injected. The resulting pressure transient was recorded for injection durations of 1 and 4 s in nonedematous lungs. The measurements were repeated after gross edema formation induced by elevated perfusion pressure. We model the interstitium as a homogeneous linearly poroelastic material and assume the initial pressure distribution due to the injection to be Gaussian. The pressure decay is inversely proportional to time, with time constant T, where T is a measure of the ratio of interstitial tissue stiffness to interstitial resistance to fluid flow. A linear regression was performed on the reciprocal of the pressure for the decaying portion of the transients to determine T. Comparing pressure transients in nonedematous and edematous lungs, we found that T was 4.0 +/- 1.4 and 1.4 +/- 0.6 s, respectively. We have shown that fluid transport through the pulmonary interstitium on a local level is sensitive to changes in interstitial stiffness and resistance. These results are consistent with the decreased stiffness and resistance in the perialveolar interstitium that accompany increased hydration.